RetrogeneDB ID: retro_mdom_1159

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:284181883..284182873(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GINM1
• Ensembl ID: ENSMODG00000016822
• Aliases: None
• Description: glycoprotein integral membrane 1 [Source:HGNC Symbol;Acc:21074]

Sequence

>retro_mdom_1159
ATGGAGGGAGGGTTACTACCCCCTCCTCTCCTGCTGCTGCTGCTCCTGGTTCCCTTGCTCCAAGCTCCTGGGTCTCTCTT
GGCTGGTGCTTCAGAGCTGCCATCAGTTCCTTCTTTCACCCAGGACAATATCAAAATTAATGTAACTACCCTGAAAGATG
ATGGGGAACTCTATGAGAAACAGGTTTTTCTTGATATTATTTGTAAAAATGGACAGATATATGTAAATTACTTTCCCTTA
AAGAGTGGTGTAACCCGATTAATGGGTGAAGGCTTCGTAGTGGAGGATAAAAATTTGGAAAACCTAAAGGTCGAAGGATA
TTTTGGAACTGTCAGCATATGGATATTAGTTCCTCAATGGCCTCTGGCATCCAGTTCCAATGTATAAATGATAGCCATTC
AAGAAGAGGTAGTAGACATTGATGGGAAAAAAGCTCAACAAAAAGTTGTCATTGAAGTTGGTATTTTTGTAAAGAACCAC
AGAGTCCACTGACATTCAAATTACACTGTTCCTTTAGAGAAAAGCATACTATATTCTATTCCAAGAGACAATGAGGTTTT
CTTTACATTTCCTCATCTTTCACAAAAAGACAGCCCTAGTGCATTGCAGACAACTAGCCAGTACCATGTCAGGAATGTGG
AAACAACCATAAATGAAGACCCATTGCCCAGAAAGTTACCCAAAACTACACTTCAAGCAGAGCCTTCATCTTCATATGAG
TTAATTTGCCAGTTGATAGAGGATTTCAGAAAATATATATGTAAATTCTGGAATAATGTTTTCCCAGTACTTTTTATATT
TATGAATATCATGGTGCTTGGAATTATAGGAGCAGCTATAGTTACAGCCATCTTGAAGGTGTTTTTCCCTTATTATAAAT
CCAAGGGAATTCTTCACTTAGATAAAGAGGACTACCATAAGTACTATCCTATTTACATTTCAGAGATGACAGAGGAACCA
AAGATTACTCTTGAAGAAAAGATATGTATT

Alignment

ORF - retro_mdom_1159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGAPPSAPLLLLVLLLLLPLLQAPGRLLAGASEPPSAASFTQDNIKINVTTLEDDGELHEKQVVLNIIY
          MEG.....PLLLL..LLL.PLLQAPG.LLAGASE.PS..SFTQDNIKINVTTL.DDGEL.EKQV.L.II.
Retrocopy MEGGLLPPPLLLL--LLLVPLLQAPGSLLAGASELPSVPSFTQDNIKINVTTLKDDGELYEKQVFLDIIC

Parental  ENGQIYVNDFPLKSGVTRIRGEAFIVEDENLENLKVKGYFGTVSIRILVHQWPLASSSNVQMIAIQEEVV
          .NGQIYVN.FPLKSGVTR..GE.F.VED.NLENLKV.GYFGTVSI.ILV.QWPLASSSNV.MIAIQEEVV
Retrocopy KNGQIYVNYFPLKSGVTRLMGEGFVVEDKNLENLKVEGYFGTVSIWILVPQWPLASSSNV*MIAIQEEVV

Parental  DIDGKKAQQKVVIEVGILVKNHRVHRRSNYTVPLEESILYSIPRDNDVFFTFPHLSQKDSPSALQTTSQY
          DIDGKKAQQKVVIEVGI.VKNHRVH..SNYTVPLE.SILYSIPRDN.VFFTFPHLSQKDSPSALQTTSQY
Retrocopy DIDGKKAQQKVVIEVGIFVKNHRVH*HSNYTVPLEKSILYSIPRDNEVFFTFPHLSQKDSPSALQTTSQY

Parental  LVRNVETTINEDPLPDKLPETPLRAEPPSSYKVICQLMEDFRKYICKFWINIFPVLFMFMNIMVLGIIGA
          .VRNVETTINEDPLP.KLP.T.L.AEP.SSY..ICQL.EDFRKYICKFW.N.FPVLF.FMNIMVLGIIGA
Retrocopy HVRNVETTINEDPLPRKLPKTTLQAEPSSSYELICQLIEDFRKYICKFWNNVFPVLFIFMNIMVLGIIGA

Parental  AIVIAILKVLFPHYESKGILHLDKVDYHKYYP-NISETTEEPKITLEEKICI
          AIV.AILKV.FP.Y.SKGILHLDK.DYHKYYP..ISE.TEEPKITLEEKICI
Retrocopy AIVTAILKVFFPYYKSKGILHLDKEDYHKYYPIYISEMTEEPKITLEEKICI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1159 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1159 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000884	1 retrocopy	retro_dnov_1058,
Monodelphis domestica	ENSMODG00000016822	1 retrocopy	retro_mdom_1159 ,
Tupaia belangeri	ENSTBEG00000009606	2 retrocopies	retro_tbel_119, retro_tbel_3851,